Boolean slow: looking for speedup ideas
Booleans are slow, heavy, error prone and produce bad topology, they also only work on meshes, requiring conversion of curves to mesh which is a destructive process.

I would suggest instead a different approach. Keep you SVG import as a live bezier curve object, use its builtin extrusion and beveling capabilities to generate geometry.

Then use the coordinates file to create bezier curve circle objects with the desired radius at the correct positions. Join these created circles back into the original SVG object. Set it as 2D curve.

If everything has been correctly designed as coherent closed splines, Blender should be able to correctly close them and represent the circles as holes.